There are two types of cilia: motile cilia, which constantly beat in a single direction, and non-motile cilia, which typically serve as sensory organelles. Along with flagella, they make up a group of organelles known as undulipodia.

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Cilia are rare in plants, occurring most notably in cycads. Protozoans (ciliates) possess motile cilia exclusively and use them for either locomotion or to simply move liquid over their surface. Some ciliates bear groups of cilia that are fused together into large mobile projections called cirri (singular, cirrus).

Larger eukaryotes, such as mammals, have motile cilia as well. Motile cilia are rarely found alone, usually present on a cell's surface in large numbers and beating in coordinated waves. In humans, for example, motile cilia are found in the lining of the trachea (windpipe), where they sweep mucus and dirt out of the lungs. In femalemammals, the beating of cilia in the Fallopian tubes moves the ovum from the ovary to the uterus.

In contrast to motile cilia, non-motile cilia usually occur one per cell. The outer segment of the rod photoreceptor cell in the human eye is connected to its cell body with a specialized non-motile cilium. The dendritic knob of the olfactory neuron, where the odorant receptors are located, is also carrying non-motile cilia (about 10 cilia / dendritic knobs). Aside from these specialized examples, almost all mammalian cells have a single non-motile primary cilium. Although the primary cilium has historically been one of the oldest cellular organelles to be studied (at least since 1898), only a small group of devotees have followed it until its importance began to become clear in the late 1990. Recent findings regarding its physiological roles in chemical sensation, signal transduction, and control of cell growth, have led scientists to acknowledge its importance in cell function and the problems caused where its development has been disrupted or inhibited (as in polycystic kidney disease).

To grow a cilium, the building blocks of the cilia such as tubulins and other partially assembled axonemal proteins are added to the ciliary tips which point away from the cell body. In most species bi-directional motility called intraflagellar transport or IFT plays an essential role to move these building materials from the cell body to the assembly site. IFT also carries the disassembled material to be recycled from the ciliary tip back to the cell body. By regulating the equilibrium between these two IFT proceses, the length of cilia can be maintained dynamically.

Ciliary defects can lead to several human diseases. Genetic mutations compromising the proper functioning of cilia can cause chronic disorders such as primary ciliary dyskinesia (PCD). In addition, a defect of the primary cilium in the renal tube cells can lead to polycystic kidney disease (PKD). In another genetic disorder called Bardet-Biedl syndrome (BBS), the mutant gene products are the components in the basal body and cilia.

Lack of functional cilia in mammalian Fallopian tubes can cause ectopic pregnancy. A fertilized ovum may not reach the uterus if the cilia are unable to move it there. In such a case, the ovum will implant in the Fallopian tubes, causing a tubal pregnancy, the most common form of ectopic pregnancy.